using emboss programs from spin

[Miguel Ortiz Lombardia]

Dear all,

I have installed on a linux system (Ubuntu 6.06):

Staden-1.7.0
EMBOSS 3.0.0

First, I had to make the iwidgets symbolic link in staden-1.7.0/lib to
point to the right place:

ln -sf /usr/lib/iwidgets4.0.1 iwidgets

I wanted to use the spin interface to run emboss programs. So I run
create_emboss_files. Because the tcl script assumes a wrong localization
of the acd files (and then it hangs indefinitely) I had to change the
create_emboss_files.tcl file so the script would know where such files
are in fact. This is what I did:

1. Comment out the procedure "proc acd_dir"

2. Down in the file change set acd_dir [acd_dir] to:
        set acd_dir /usr/local/share/EMBOSS/acd

After doing this, the acd files are found and some of them processed.
Others produce errors, I can post these errors if someone is interested.

To use staden with emboss, I issued:

export STADENROOT=/usr/local/staden-1.7.0
. $STADENROOT/staden.profile
export EMBOSS_DATA=/usr/local/share/EMBOSS/data

But then I get many "qualifier" errors. I think this is because the
spin_emboss package instead of the spin2_emboss one is being used. I
checked at least that for the EMBOSS program "matcher".

Could someone tell me how to enforce the use of spin2_emboss?

Thank you very much in advance,


Miguel
--
Miguel Ortiz Lombardía
Centro de Investigaciones Oncológicas
C/ Melchor Fernández Almagro, 3
28029 Madrid, Spain
Tel. [phone]
Fax. [phone]
email: molatwork@...
www: http://www.ysbl.york.ac.uk/~mol/
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Le travail est ce que l'homme a trouvé de mieux
pour ne rien faire de sa vie.                          (Raoul Vaneigem)

**NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
**CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.

_______________________________________________
Staden mailing list
Staden@...
http://www.bio.net/biomail/listinfo/staden